Re: CCL:Van Der Waals Collapse

[states %! at !% ibc.wustl.edu (David J. States)]

 |> From: Hodgkin, Ed
 |>
 |> It is well known that molecular mechanics force fields favour 'folded'
 |> conformations which derive stability from large Van Der Waals terms.
 |> One could coin the phrase "Van Der Waals Collapse" to describe
 this
 |> effect....
 From the earliest days of charmm development, this has been a concern.
 Globular proteins simulated in vacuo shrink when "true" atomic radii
 are used as the basis for nonbonded interaction parameters.
 Swaminathan spent alot of time working on a compensating force term,
 but I don't know what became of the work.  The most direct way to
 control for the self-association of peptide chains is to do a
 simulation that includes solvation explicitly.  Note that if you do
 this as a water droplet rather than a periodic box the internal
 pressure generated by surface tension is enormous so the system will
 still collapse some compared to physiologic conditions.
 David States